Does COVID-19 infect peripheral blood cells?

The emergence of the novel coronavirus outbreak in December 2019 was followed by its spread on a global scale unparalleled in the last 100 years. At present, it has claimed over 322,000 lives the world over, with over 4.88 million cases having tested positive.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequence was first uploaded in early 2020, but as of now, over 17,000 genomes have been sequenced from viral strains isolated all over the world. This allows for rapid RNA screening in human tissues as well as environmental samples.

Detection of Virus in Human Blood or Blood Cells

The current study by researchers in Cairo, Egypt, and published on the preprint server medRxiv* was designed to test for the presence of the virus in human blood or any blood cells, which could allow the virus to hide from the immune system or to be trafficked to other organs. It is especially relevant given some (doubtful) reports that the virus could infect lymphocytes.

Other scientists have claimed that the virus perhaps attacks hemoglobin, or that it is to be found in the blood of infected patients, or the peripheral blood mononuclear cells (PMBCs), as is the case with other infectious viruses like hepatitis B, hepatitis C or HIV.

The current study, therefore, used computational analysis on three genome sequences from PBMCs from active COVID-19 patients, three from healthy donor PBMCs, and two from bronchoalveolar lavage fluid (BAL) from patients. They found that traces and large amounts of SARS-CoV-2 RNA were found in the PMBCs and BAL, respectively.

Viral RNA in Blood Cells

The results showed that the BAL and PBMC samples were widely separated, as expected, while the PBMCs from healthy and patient samples were slightly separated for the most part. Viral RNA was present in all the BALF sequences at 2.15% of the total reads (median). The PBMC of one patient also showed two reads that matched the SAR-CoV-2 protein and surface glycoprotein.

Earlier studies showed that with the use of RT-PCR, CoV-RNA was found in plasma samples from COVID-19 patients, but they did not confirm the presence of infectious viral particles in the blood. For this reason, they called their finding ‘RNAemia’ rather than viremia.

The current report is, however, the first to show the presence of viral RNA in PBMC. In fact, a prior study that examined RNA isolated from PBMC made it clear that no viral sequences were found.
The researchers used high-throughput sequencing, which has been demonstrated to be effective in identifying and measuring the number of viral particles in the blood. For this reason, they used this method to do a comprehensive search for viral RNA sequences within the only public dataset now available. They found that viral RNA was present within all BAL samples, at a concentration of 2.15% of the total RNA. Two RNA reads corresponded to the SARS-CoV-2 genome. However, as expected, the PBMC from the controls did not contain any RNA.

Implications

Though the amount of viral RNA is small, it is undoubtedly that of the SARS-CoV-2. One of the reads encodes a polyprotein, which takes part in viral transcription and replication, and which is the largest of the coronavirus proteins. Another encoded the spike protein, which is responsible for the viral entry into human cells that carry the ACE2 molecule receptor.

The possibility is always alive that the viral RNA reads are the result of cross-contamination or one barcode bleeding into another. However, this is a rare chance because none of the control samples showed similar correspondence. Again, they could be the result of virus sampling by antigen-presenting cells, especially dendritic cells, or virus presentation to T cells, which form part of the PBMC population.

There is a third possibility, which can be analyzed only with a much larger number of samples. This is that the virus may have been engulfed either on purpose or by accident by one of the PBMCs. This occurrence could be one mechanism for chronic SARS-CoV-2 infection, but the theory must be tested rigorously.

One hypothesis that is not supported by the current experiment is T cell targeting by the virus in vivo, which arose from an earlier cell culture experiment using pseudotyped viruses.

The current experiment will help to take the present understanding of the progress and replication of the SARS-CoV-2 infection in humans.

 

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Face Mask that Lights Up When it Senses Coronavirus: A Possible Alternative for Antibody Tests and Temperature Checks

Bioengineers from MIT and Harvard have been working on developing sensors that can detect viruses such as Ebola and Zika for the last six years. Their hard work has since then progressed and are now adopting their technology to aid in the fight against coronavirus.

James Collins, a professor of Biological Engineering at MIT, is considered a pioneer of synthetic biology. He has been working on innovations that would be helpful for pandemics years before the coronavirus surfaced.

In 2014, his bioengineering team at MIT began developing sensors that could recognize the presence of the Ebola virus when freeze-dried into a piece of paper. Their study was then published in the journal Cell back in 2016.

The team is now updating its technology to cater to the current pandemic the world is facing, which is the coronavirus. They are currently developing a face mask that gives off a fluorescent signal when the wearer is detected to have the virus through breathing, coughing, or sneezing through the mask.
Promising Results

Collins says their lab's current project is still in its infancy, but already shows promising results as it can detect coronavirus through a person's saliva. The sensor would give off a signaling glow once the virus is detected in a person's saliva.

According to Collins, the sensors are made up of DNA and RNA that bind to a virus. The sensor is then freeze-dried into a cloth-like material using a freeze-drier, which sucks the moisture out of the material without damaging it. The sensor can stay embedded in the mask at room temperature for many months, giving it a considerably longer shelf life.

To be activated, the sensors need moisture and the detection of a virus' genetic sequence. A laboratory in Shanghai successfully sequenced the coronavirus genome back in January.

Collins said the sensors only needed to analyze a small fragment of the sequence to detect the virus. Once it does, it gives off a lighting signal within one to three hours.

Additionally, he said the signal isn't visible to the naked eye, which is why his lab uses a fluorimeter to measure the light. In public settings, he noted that public officials could use handheld fluorometers to scan people's masks.

Alternative For Antibody Tests and Temperature Checks
If the team's technology proves to be successful, it could address imperfections correlated with other screening methods like temperature checks or antibody tests.

Collins says that he envisions that it could be used in airports, commuting to and from work to home, and in hospitals as a pre-screen for patients. He said that doctors could even use the masks to diagnose patients without having to send samples to the laboratory.

The sensors might offer a quicker, cheaper, and more sensitive type of detection for the coronavirus than the traditional diagnostic tests, according to Collins. Because the sensors developed by the researchers are highly specific, they are capable of detecting different strains of a virus.

This is especially helpful in the case of the coronavirus since scientists have traced coronavirus strains back to two main origins. One of the strains has said to come from Asia, while another strain has become more prevalent in Australia, Europe, and North America.

The masks might even prove to detect coronavirus better than temperature checks, as some COVID-19 patients appear to either be asymptomatic, pre-symptomatic or experiencing other symptoms without having a fever. Collins thinks their technology could provide better results as it detects the virus itself and not the presenting signs.

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Johns Hopkins researchers make progress in the development of noninvasive urine test for prostate cancer

Researchers at the Johns Hopkins Kimmel Cancer Center have made significant progress toward development of a simple, noninvasive liquid biopsy test that detects prostate cancer from RNA and other specific metabolic chemicals in the urine.

A description of their findings appears in the Feb. 28 issue of the journal Scientific Reports.

The investigators emphasize that this is a proof-of-principle study for the urine test, and it must be validated in additional, larger studies before it is ready for clinical use.

The researchers used RNA deep-sequencing and mass spectrometry to identify a previously unknown profile of RNAs and dietary byproducts, known as metabolites, among 126 patients and healthy, normal people. The cohort included 64 patients with prostate cancer, 31 with benign prostatic hyperplasia and prostatitis diseases, and 31 healthy people with none of these conditions. RNA alone was not sufficient to positively identify the cancer, but addition of a group of disease-specific metabolites provided separation of cancer from other diseases and healthy people.

"A simple and noninvasive urine test for prostate cancer would be a significant step forward in diagnosis. Tissue biopsies are invasive and notoriously difficult because they often miss cancer cells, and existing tests, such as PSA (prostate-specific antigen) elevation, are not very helpful in identifying cancer," says Ranjan Perera, Ph.D., the study's senior author. Perera is also the director of the Center for RNA Biology at Johns Hopkins All Children's Hospital, a senior scientist at the Johns Hopkins All Children's Cancer & Blood Disorders Institute and the Johns Hopkins All Children's Institute for Fundamental Biomedical Research, and an associate professor of oncology at the Johns Hopkins University School of Medicine and Johns Hopkins Kimmel Cancer Center member.

We discovered cancer-specific changes in urinary RNAs and metabolites that -- if confirmed in a larger, separate group of patients -- will allow us to develop a urinary test for prostate cancer in the future."  Bongyong Lee, Ph.D., study's first author and a senior scientist at the Cancer & Blood Disorders Institute.

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Researchers discover vaccine to treat herpes

Researchers have discovered a new vaccine which is proving to be effective in combating herpes virus.

In the study, researchers delivered the Penn-developed vaccine to 64 mice and then exposed them to genital herpes. After 28 days, 63 of the mice were found to have sterilising immunity, meaning there was no trace of herpes infection or disease after the exposure.

Similarly, 10 guinea pigs, which have responses to herpes infections that more closely resemble that of humans, were also given the vaccine and exposed to the virus.

No animal developed genital lesions and only two showed any evidence that they became infected, but the infection was not in a form that animals could transmit the virus, reported the study.

"We're extremely encouraged by the substantial immunising effect our vaccine had in these animal models," said the study's principal investigator Harvey Friedman, MD, a professor of Infectious Diseases.

"Based on these results, it is our hope that this vaccine could be translated into human studies to test both the safety and efficacy of our approach," added Friedman.

Building on the approaches of much cutting-edge cancer and immunotherapy researchers, the Penn team filled their vaccine with specific messenger RNA (mRNA), which can create proteins necessary for a strong immune response.

This vaccine stimulates three types of antibodies: one that blocks the herpes virus from entering cells, and two others that ensure the virus doesn't "turn off" innate immune system protective functions.

This approach differs from other herpes vaccines, which often only rely on blocking the virus's entry as the mode to attack the virus.

Genital herpes also called Herpes simplex virus type 2 or HSV-2 is the most common sexually-transmitted disease. Approximately 14 per cent of Americans ages 14 to 59, and 11 per cent of people in the same age range across the world are infected. HSV-2 may lead to painful sores, which can spread to other areas of the body.

The virus increases one's risk of contracting HIV and infected pregnant women may pass herpes onto their fetus, or more commonly, to their baby during delivery.

"Along with physical symptoms, HSV-2 takes an emotional toll," said the researcher. "People worry over the transmission of the disease, and it can certainly have a negative effect on intimate relationships."

Since herpes is so widespread but also often undetected, as it is only visible during an outbreak, researchers say a successful vaccine would be invaluable to many adults across the world.


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Study sheds light on genetic overlap between major psychiatric disorders

Most medical disorders have well-defined physical characteristics seen in tissues, organs and bodily fluids. Psychiatric disorders, in contrast, are not defined by such pathology, but rather by behavior.

A  study, has found that autism, schizophrenia and bipolar disorder share some physical characteristics at the molecular level, specifically, patterns of gene expression in the brain. Researchers also pinpointed important differences in these disorders' gene expression.

"These findings provide a molecular, pathological signature of these disorders, which is a large step forward," said a distinguished professor of neurology, psychiatry and human genetics. "The major challenge now is to understand how these changes arose."

Researchers know that certain variations in genetic material put people at risk for psychiatric disorders, but DNA alone doesn't tell the whole story. Every cell in the body contains the same DNA; RNA molecules, on the other hand, play a role in gene expression in different parts of the body, by "reading" the instructions contained within DNA.

The study's lead author,  reasoned that taking a close look at the RNA in human brain tissue would provide a molecular profile of these psychiatric disorders.

Researchers analyzed the RNA in 700 tissue samples from the brains of deceased subjects who had autism, schizophrenia, bipolar disorder, major depressive disorder or alcohol abuse disorder, comparing them to samples from brains without psychiatric disorders.

The molecular pathology showed significant overlap between distinct disorders, such as autism and schizophrenia, but also specificity, with major depression showing molecular changes not seen in the other disorders.

"We show that these molecular changes in the brain are connected to underlying genetic causes, but we don't yet understand the mechanisms by which these genetic factors would lead to these changes," the Prof. said. "So, although now we have some understanding of causes, and this new work shows the consequences, we now have to understand the mechanisms by which this comes about, so as to develop the ability to change these outcomes." 

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Researchers uncover molecular mechanisms linked to autism and schizophrenia

Since the completion of the groundbreaking Human Genome Project in 2003, researchers have discovered changes to hundreds of places in the DNA, called genetic variants, associated with psychiatric diseases such as autism spectrum disorder and schizophrenia. Now, new findings from a major study has linked many of these changes in DNA to their molecular effect in the brain, revealing new mechanisms of diseases. 

In the new papers, researchers and collaborators from more than a dozen institutions from around the world provide the largest-ever datasets on the molecular workings of the brain. The findings provide a roadmap for development of a new generation of therapies for psychiatric conditions.

"This work provides several missing links necessary for understanding the mechanisms of psychiatric diseases," said  a senior author.

During the last decade, scientists have conducted genetic studies of people with psychiatric diseases, comparing the results to healthy individuals to find genes that have different sequences in those with disease. Often, however, their findings led to more questions than answers. Scientists not only discovered genes linked to the diseases, they also uncovered hundreds of areas of DNA found in between genes, called regulatory DNA, that also seemed to have an association.

Scientists know these sections of DNA can control when, where and how genes are turned on and off in many ways. However, figuring out which "regulatory regions" affect which genes— and therefore the RNA and proteins encoded by the genes— is not straightforward.

In 2015, researchers at 15 institutions around the country, came together in the Consortium to study in more detail the brain's regulatory DNA. An earlier project, known as ENCODE, already had uncovered the roles sections of regulatory DNA, but it was clear that these might be different in the brain than other organs. The PsychENCODE has analyzed not just genetic variants linked to psychiatric diseases, but also patterns of RNA and proteins in 2,188 brain bank samples from both healthy individuals and those with a psychiatric disorder.

In one new paper, the researchers describe this new data, which helps explain the roles of tens of thousands of sections of regulatory DNA in affecting RNA and proteins in the brain. The data also reveals which genes are most often expressed at the same time as each other, suggesting new biological processes and pathways. The dataset—essentially a detailed model of the inner molecular workings of the human brain— is now publicly available as a starting point for other researchers to mine mechanisms of disease and potential drug targets.

"This resource is so vast that you can start by choosing one interesting disease associated genetic variant and begin digging into that and discovering how it impacts molecular networks in the brain," he said. "Having robust data of this scope provides a foundation for countless new studies."

In a second paper, assistant professor of psychiatry and biobehavioral Sciences  and other collaborators, used that new data to look specifically at how RNA molecules are dysregulated—either present at higher levels, lower levels, or in altered conformations— in autism spectrum disorder, schizophrenia and bipolar disorder.

Using nearly 1,700 brain bank samples, the researchers revealed thousands of RNA molecules that are either spliced differently— with different sections of genetic material—or present at higher or lower levels in the brains of people with one of the psychiatric diseases.

"You can't look at the brain under a microscope and see substantial differences in these  disorders" the Prof. said. "But we've now shown that if you look finely at patterns of how genes are expressed, you see pathways that are clearly dysregulated."

Among the surprises in the data— altered levels of RNA linked to neuroinflammation and the brain's immune cells showed very different trajectories in people with schizophrenia, autism spectrum disorder and bipolar disorder.

Additionally, the study showed the importance of looking at individual cell types within the brain when parsing the new RNA data— in some cases, alternately spliced RNA was linked to disease but only when the RNA was found in certain cell types and not others.

Finally, new genes were implicated in the diseases based on the RNA results; five were linked to autism spectrum disorder, 11 to bipolar disorder, and 56 to schizophrenia.

Once again, the data is mostly important as a jumping off point for future studies, the researchers said.

"This is the tip of the iceberg," a Prof. said. "The ability to compile together 2,000 brains has been revolutionary in terms of revealing new genetic mechanisms, but it also points to how much we don't know." 

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